Despite the historic merging, dissension between the kwans did not end at the 1955 meeting. There was still much animosity between the various masters.

In November 1958, the Korea Tang-Soo Do Association applied for membership to the Korea Amateur Sports Association (KASA) but it was denied because there was a rival organization, the Korea Kong-Soo Do Association. The KASA agreed to accept the application only if both organizations united as one. Representatives of the two associations met and agreed to unite under the name Korea Soo-Bahk-Do Association. Finally, on September 3, 1959, representatives of the six Kwans agreed to unite under the name Korea Taekwondo Association and Choi was elected its president, however, this organization would not last very long.

General Choi was elected president because of his position as a general in the Korean Army (under a military regime) and because he promised the heads of the original kwans that he would promote Taekwondo. However, the country was poor and had other more pressing concerns than spending valuable resources on martial arts. Because the government failed to come through with the things Choi had promised, he fell into disfavor with the other kwan heads.

On September 19, 1961, by presidential decree, the newly formed association became the Korea Tae-Soo-Do Association. This is considered the 'true' inauguration of the KTA. Mr. Chae Myung Shin (a non-martial artist) was chosen the first KTA president, serving until January 15, 1965 when he was replaced by General Choi (from September 1961 until January 1965, Choi had not served in the Korea Tae-Soo-Do Association as either an officer or president). Choi served as president for one year, during which he convinced the association to change its name back to the Korea Taekwondo Association. The name change was completed on August 5, 1965. On January 30, 1966, Byung Jik Ro, founder of the Song Moo Kwan was elected president of the KTA.